The problem appears to be that the installer for the native messaging host is not registering the manifest file in the registry properly.
see: https://developer.chrome.com/extensions/nativeMessaging#native-messaging-host-location
Manually creating the registry entry fixed the problem for me.
# from a cmd prompt or Run command
REG ADD "HKCU\Software\Google\Chrome\NativeMessagingHosts\com.sean.consoleread" /ve /t REG_SZ /d "C:\Users\<username>\AppData\Roaming\AutoIt3\Chrome Native Messaging Host\manifest.json" /f
